Proceedings of the 15th Workshop on Biomedical Natural Language Processing

Proceedings of the 15th Workshop on Biomedical Natural Language Processing University of Colorado School of MedicineKevin Bretonnel Cohen National Library of MedicineDina Demner-Fushman UKSophia Ananiadou, National Centre for Text Mining and University of Manchester JapanJun-ichi Tsujii, National Institute of Advanced Industrial Science and Technology August 2016

Berlin, Germany

Association for Computational Linguistics http://anthology.aclweb.org/W16-29 book BioNLP16:2016 A Machine Learning Approach to Clinical Terms Normalization JoseCastano María LauraGambarte Hee JoonPark Maria del PilarAvila Williams DavidPerez FernandoCampos DanielLuna SoniaBenitez HernanBerinsky SofíaZanetti Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 1–11 http://anthology.aclweb.org/W16-2901 inproceedings castano-EtAl:2016:BioNLP16 Improved Semantic Representation for Domain-Specific Entities Mohammad TaherPilehvar NigelCollier Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 12–16 http://anthology.aclweb.org/W16-2902 inproceedings pilehvar-collier:2016:BioNLP16 Identification, characterization, and grounding of gradable terms in clinical text ChaitanyaShivade Marie-Catherinede Marneffe EricFosler-Lussier Albert M.Lai Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 17–26 http://anthology.aclweb.org/W16-2903 inproceedings shivade-EtAl:2016:BioNLP16 Graph-based Semi-supervised Gene Mention Tagging GolnarSheikhshab ElizabethStarks AlyKarsan AnoopSarkar InancBirol Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 27–35 http://anthology.aclweb.org/W16-2904 inproceedings sheikhshab-EtAl:2016:BioNLP16 Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses DayneFreitag JohnNiekrasz Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 36–45 http://anthology.aclweb.org/W16-2905 inproceedings freitag-niekrasz:2016:BioNLP16 Inferring Implicit Causal Relationships in Biomedical Literature HalilKilicoglu Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 46–55 http://anthology.aclweb.org/W16-2906 inproceedings kilicoglu:2016:BioNLP16 SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction Marco A.Valenzuela-Escárcega GusHahn-Powell DaneBell MihaiSurdeanu Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 56–65 http://anthology.aclweb.org/W16-2907 inproceedings valenzuelaescarcega-EtAl:2016:BioNLP16 Character based String Kernels for Bio-Entity Relation Detection RitambharaSingh YanjunQi Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 66–71 http://anthology.aclweb.org/W16-2908 inproceedings singh-qi:2016:BioNLP16 Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge AmySiu PatrickErnst GerhardWeikum Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 72–76 http://anthology.aclweb.org/W16-2909 inproceedings siu-ernst-weikum:2016:BioNLP16 Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts StephanTulkens SimonSuster WalterDaelemans Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 77–82 http://anthology.aclweb.org/W16-2910 inproceedings tulkens-suster-daelemans:2016:BioNLP16 Unsupervised Document Classification with Informed Topic Models TimothyMiller DmitriyDligach GuerganaSavova Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 83–91 http://anthology.aclweb.org/W16-2911 inproceedings miller-dligach-savova:2016:BioNLP16 Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes SumithraVelupillai Danielle LMowery MikeConway JohnHurdle BrentKious Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 92–101 http://anthology.aclweb.org/W16-2912 inproceedings velupillai-EtAl:2016:BioNLP16 Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute KaiHakala SuwisaKaewphan TapioSalakoski FilipGinter Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 102–107 http://anthology.aclweb.org/W16-2913 inproceedings hakala-EtAl:2016:BioNLP16 Improving Temporal Relation Extraction with Training Instance Augmentation ChenLin TimothyMiller DmitriyDligach StevenBethard GuerganaSavova Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 108–113 http://anthology.aclweb.org/W16-2914 inproceedings lin-EtAl:2016:BioNLP16 Using Centroids of Word Embeddings and Word Mover's Distance for Biomedical Document Retrieval in Question Answering Georgios-IoannisBrokos ProdromosMalakasiotis IonAndroutsopoulos Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 114–118 http://anthology.aclweb.org/W16-2915 inproceedings brokos-malakasiotis-androutsopoulos:2016:BioNLP16 Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway MichaelSpranger SucheendraPalaniappan SamikGosh Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 119–127 http://anthology.aclweb.org/W16-2916 inproceedings spranger-palaniappan-gosh:2016:BioNLP16 Construction of a Personal Experience Tweet Corpus for Health Surveillance KeyuanJiang RicardoCalix MatrikaGupta Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 128–135 http://anthology.aclweb.org/W16-2917 inproceedings jiang-calix-gupta:2016:BioNLP16 Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification NutLimsopatham NigelCollier Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 136–140 http://anthology.aclweb.org/W16-2918 inproceedings limsopatham-collier:2016:BioNLP16 PubTermVariants: biomedical term variants and their use for PubMed search LanaYeganova WonKim SunKim RezartaIslamaj Doğan WanliLiu Donald CComeau ZhiyongLu W JohnWilbur Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 141–145 http://anthology.aclweb.org/W16-2919 inproceedings yeganova-EtAl:2016:BioNLP16 This before That: Causal Precedence in the Biomedical Domain GusHahn-Powell DaneBell Marco A.Valenzuela-Escárcega MihaiSurdeanu Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 146–155 http://anthology.aclweb.org/W16-2920 inproceedings hahnpowell-EtAl:2016:BioNLP16 Syntactic methods for negation detection in radiology reports in Spanish VivianaCotik VanesaStricker JorgeVivaldi HoracioRodriguez Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 156–165 http://anthology.aclweb.org/W16-2921 inproceedings cotik-EtAl:2016:BioNLP16 How to Train good Word Embeddings for Biomedical NLP BillyChiu GamalCrichton AnnaKorhonen SampoPyysalo Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 166–174 http://anthology.aclweb.org/W16-2922 inproceedings chiu-EtAl:2016:BioNLP16 An Information Foraging Approach to Determining the Number of Relevant Features BrianConnolly BenjaminGlass JohnPestian Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 175–180 http://anthology.aclweb.org/W16-2923 inproceedings connolly-glass-pestian:2016:BioNLP16 Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians Brian E.Chapman Danielle LMowery EvanNarasimhan NeelPatel WendyChapman MartaHeilbrun Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 181–185 http://anthology.aclweb.org/W16-2924 inproceedings chapman-EtAl:2016:BioNLP16 Building a dictionary of lexical variants for phenotype descriptors SimonKocbek TudorGroza Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 186–190 http://anthology.aclweb.org/W16-2925 inproceedings kocbek-groza:2016:BioNLP16 Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections OlofJacobson HerculesDalianis Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 191–195 http://anthology.aclweb.org/W16-2926 inproceedings jacobson-dalianis:2016:BioNLP16 Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning GenevieveGorrell SherifatOduola AngusRoberts TomCraig CraigMorgan RobStewart Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 196–205 http://anthology.aclweb.org/W16-2927 inproceedings gorrell-EtAl:2016:BioNLP16 Relation extraction from clinical texts using domain invariant convolutional neural network SunilSahu AshishAnand KrishnadevOruganty MahanandeeshwarGattu Proceedings of the 15th Workshop on Biomedical Natural Language Processing August 2016

Berlin, Germany

Association for Computational Linguistics 206–215 http://anthology.aclweb.org/W16-2928 inproceedings sahu-EtAl:2016:BioNLP16